Updates for pipeline running

[MattWellie]

Fixes

• We can't run AIP in production-pipelines

Proposed Changes

• Updates the run preparation script (get participants, HPOs, hpo-matched panels) to use GQL. This cuts out a lot of logic (looking up external IDs separately etc.)
• Updates the hail labelling script to take an explicit output argument (so that it can be passed in to a pipeline stage)
• Changes config to use status_reporter in line with production pipelines
• Tests adjusted to new GQL logic
• Plink file renamed to Pedigree. Not sure why I ever called it --plink
• CHANGELOG updated with the massive number of changes

Checklist

• [x] Related Issue created
• [x] Tests
• [x] Linting checks pass

Twinned with:

• https://github.com/populationgenomics/production-pipelines/pull/484
• https://github.com/populationgenomics/production-pipelines-configuration/pull/1

[MattWellie]

Still need to add some config adjustment - ideally consolidating the dataset_specific and cohorts sections of the config file into one region